[med-svn] [Git][med-team/gemma][master] 3 commits: Revert changes to enable a smallest changes upload to fix bug #982692
Andreas Tille
gitlab at salsa.debian.org
Wed Apr 7 15:48:44 BST 2021
Andreas Tille pushed to branch master at Debian Med / gemma
Commits:
d57a77f0 by Andreas Tille at 2021-04-07T16:20:35+02:00
Revert changes to enable a smallest changes upload to fix bug #982692
- - - - -
e4e9da9d by Andreas Tille at 2021-04-07T16:28:07+02:00
Follow upstream suggestion to comment some tests that might fail due to some floating point rounding
- - - - -
e665bff6 by Andreas Tille at 2021-04-07T16:39:30+02:00
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- + debian/patches/exclude_assertions_failing_under_some_circumstances.patch
- − debian/patches/hardening.patch
- debian/patches/series
- debian/rules
- debian/tests/run-sample-analysis
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,11 @@
-gemma (0.98.4+dfsg-3) UNRELEASED; urgency=medium
+gemma (0.98.4+dfsg-3) unstable; urgency=medium
* Team upload.
- * Enable hardening
+ * Follow upstream suggestion to comment some tests that might fail due
+ to some floating point rounding
+ Closes: #982692
- -- Andreas Tille <tille at debian.org> Mon, 22 Mar 2021 14:38:26 +0100
+ -- Andreas Tille <tille at debian.org> Wed, 07 Apr 2021 16:28:38 +0200
gemma (0.98.4+dfsg-2) unstable; urgency=medium
=====================================
debian/patches/exclude_assertions_failing_under_some_circumstances.patch
=====================================
@@ -0,0 +1,53 @@
+Description: Follow upstream suggestion to comment some tests that might fail due
+ to some floating point rounding
+Bug-Debian: https://bugs.debian.org/982692
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 07 Apr 2021 16:25:29 +0200
+
+--- a/test/dev_test_suite.sh
++++ b/test/dev_test_suite.sh
+@@ -79,7 +79,7 @@ testBXDLMMLikelihoodRatio() {
+
+ outfn=output/$outn.assoc.txt
+ assertEquals "73180" `wc -w < $outfn`
+- assertEquals "3088458213" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn`
++ #assertEquals "3088458213" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn`
+ }
+
+ testBXDLMM9LikelihoodRatio() {
+@@ -96,7 +96,7 @@ testBXDLMM9LikelihoodRatio() {
+
+ outfn=output/$outn.assoc.txt
+ assertEquals "80498" `wc -w < $outfn`
+- assertEquals "3088496565" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn`
++ #assertEquals "3088496565" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn`
+ }
+
+ testCenteredRelatednessMatrixissue188() {
+@@ -113,7 +113,7 @@ testLMMissue188() {
+ $gemma $gemmaopts -b data/issue188/2000 -lmm 2 -k output/$outn.cXX.txt -maf 0.01 -o $outn -n 1
+ assertEquals 0 $?
+ outfn=output/$outn.assoc.txt
+- assertEquals "338154001.76" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
++ #assertEquals "338154001.76" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ }
+
+ testCenteredRelatednessMatrixKLOCO1() {
+@@ -147,7 +147,7 @@ testUnivariateLinearMixedModelLOCO1() {
+ assertEquals 0 $?
+ outfn=output/$outn.assoc.txt
+ assertEquals "68" `wc -l < $outfn`
+- assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
++ #assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ }
+
+ testPlinkCenteredRelatednessMatrixKLOCO1() {
+@@ -188,7 +188,7 @@ testPlinkUnivariateLinearMixedModelLOCO1
+ assertEquals 0 $?
+ outfn=output/$outn.assoc.txt
+ assertEquals "68" `wc -l < $outfn`
+- assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
++ #assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ }
+
+
=====================================
debian/patches/hardening.patch deleted
=====================================
@@ -1,23 +0,0 @@
-Description: Propagate LDFLAGS to enable hardening
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 22 Mar 2021 14:38:26 +0100
-
---- a/Makefile
-+++ b/Makefile
-@@ -219,14 +219,14 @@ debug: $(OUTPUT)
- $(shell bash $(VGEN) $(GUIX_PROFILE) > src/version.h)
-
- $(OUTPUT): $(OBJS)
-- $(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT)
-+ $(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT) $(LDFLAGS)
-
- $(OBJS): $(HDR)
-
- .SUFFIXES : .cpp .c .o $(SUFFIXES)
-
- ./bin/unittests-gemma: $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(OBJS)
-- $(CPP) $(CPPFLAGS) $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(filter-out src/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma
-+ $(CPP) $(CPPFLAGS) $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(filter-out src/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma $(LDFLAGS)
-
- unittests: all ./bin/unittests-gemma
- ./bin/unittests-gemma
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,4 @@
+exclude_assertions_failing_under_some_circumstances.patch
Reproducible_builds.patch
no-lquadmath.patch
Makefile.patch
-hardening.patch
=====================================
debian/rules
=====================================
@@ -1,7 +1,7 @@
#!/usr/bin/make -f
export DH_VERBOSE = 1
-export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen
export DEB_CXXFLAGS_MAINT_APPEND = -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen
=====================================
debian/tests/run-sample-analysis
=====================================
@@ -17,6 +17,8 @@ gemma -g mouse_hs1940.geno.txt.gz -p mouse_hs1940.pheno.txt \
-a mouse_hs1940.anno.txt -gk -o mouse_hs1940
hostarch=$(dpkg-architecture -qDEB_HOST_ARCH)
+
+# Ignore single test on armhf and i386 (see bug #972553)
if [ "$hostarch" = "armhf" ] ; then
echo "Do only one test for $hostarch to reduce test time (see bug #985004)"
exit 0
View it on GitLab: https://salsa.debian.org/med-team/gemma/-/compare/f7047363b8fcaf1eefde9caa80d5ae88076f808a...e665bff6d93fa88e71353d9bc8f41629758247d7
--
View it on GitLab: https://salsa.debian.org/med-team/gemma/-/compare/f7047363b8fcaf1eefde9caa80d5ae88076f808a...e665bff6d93fa88e71353d9bc8f41629758247d7
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20210407/d56c18cf/attachment-0001.htm>
More information about the debian-med-commit
mailing list